Multiple sequence alignment - TraesCS4B01G384000

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS4B01G384000 chr4B 100.000 3187 0 0 1 3187 663519703 663522889 0.000000e+00 5886.0
1 TraesCS4B01G384000 chr4B 91.694 1842 130 11 513 2334 662720981 662719143 0.000000e+00 2532.0
2 TraesCS4B01G384000 chr4B 92.084 1819 107 9 712 2496 663462565 663464380 0.000000e+00 2527.0
3 TraesCS4B01G384000 chr4B 95.385 910 31 4 682 1581 663621287 663622195 0.000000e+00 1437.0
4 TraesCS4B01G384000 chr4B 96.921 682 20 1 1599 2280 663629235 663629915 0.000000e+00 1142.0
5 TraesCS4B01G384000 chr4B 90.909 550 38 10 2647 3187 663464509 663465055 0.000000e+00 728.0
6 TraesCS4B01G384000 chr4B 88.889 549 34 15 2427 2955 662714915 662714374 0.000000e+00 651.0
7 TraesCS4B01G384000 chr4B 92.344 209 14 2 2954 3160 662714153 662713945 2.400000e-76 296.0
8 TraesCS4B01G384000 chr4B 90.385 208 12 4 513 717 663461699 663461901 1.880000e-67 267.0
9 TraesCS4B01G384000 chr4B 96.040 101 4 0 2239 2339 663629916 663630016 7.070000e-37 165.0
10 TraesCS4B01G384000 chr4B 95.050 101 5 0 1 101 663621134 663621234 3.290000e-35 159.0
11 TraesCS4B01G384000 chr4B 96.512 86 3 0 264 349 662721081 662720996 3.310000e-30 143.0
12 TraesCS4B01G384000 chr4B 91.489 94 5 1 2196 2289 662788660 662788750 3.340000e-25 126.0
13 TraesCS4B01G384000 chr4B 91.489 94 5 3 2196 2289 662931828 662931918 3.340000e-25 126.0
14 TraesCS4B01G384000 chr4B 90.909 88 5 1 2196 2283 663551739 663551823 7.220000e-22 115.0
15 TraesCS4B01G384000 chr4B 94.444 72 3 1 2359 2429 662718546 662718475 3.360000e-20 110.0
16 TraesCS4B01G384000 chr4B 96.296 54 1 1 49 101 663461548 663461601 1.570000e-13 87.9
17 TraesCS4B01G384000 chr4B 94.444 54 2 1 49 101 662721133 662721080 7.330000e-12 82.4
18 TraesCS4B01G384000 chr4B 100.000 38 0 0 3150 3187 662713942 662713905 1.590000e-08 71.3
19 TraesCS4B01G384000 chr4B 96.875 32 0 1 1577 1608 663627475 663627505 6.000000e-03 52.8
20 TraesCS4B01G384000 chr5B 92.778 180 12 1 89 268 622039379 622039201 3.150000e-65 259.0
21 TraesCS4B01G384000 chr5B 94.048 168 9 1 98 265 595152695 595152861 1.470000e-63 254.0
22 TraesCS4B01G384000 chr5B 92.529 174 12 1 92 265 217679044 217679216 6.830000e-62 248.0
23 TraesCS4B01G384000 chr5B 92.025 163 13 0 346 508 322206668 322206506 2.470000e-56 230.0
24 TraesCS4B01G384000 chr5B 91.358 162 14 0 348 509 405526489 405526328 4.140000e-54 222.0
25 TraesCS4B01G384000 chr5D 93.529 170 10 1 99 268 5556828 5556660 5.280000e-63 252.0
26 TraesCS4B01G384000 chr3B 93.529 170 10 1 99 268 246304015 246303847 5.280000e-63 252.0
27 TraesCS4B01G384000 chr3B 92.529 174 11 2 100 272 245979345 245979173 6.830000e-62 248.0
28 TraesCS4B01G384000 chr1B 93.064 173 11 1 94 266 442068963 442069134 5.280000e-63 252.0
29 TraesCS4B01G384000 chr1B 93.023 172 11 1 98 269 259414337 259414507 1.900000e-62 250.0
30 TraesCS4B01G384000 chr1B 90.854 164 15 0 348 511 605929281 605929118 1.490000e-53 220.0
31 TraesCS4B01G384000 chr6B 93.023 172 11 1 97 268 238152483 238152653 1.900000e-62 250.0
32 TraesCS4B01G384000 chr6B 91.925 161 13 0 348 508 467394465 467394625 3.200000e-55 226.0
33 TraesCS4B01G384000 chr2A 91.515 165 14 0 348 512 700986074 700986238 8.890000e-56 228.0
34 TraesCS4B01G384000 chr7D 91.358 162 12 2 348 508 111478879 111478719 1.490000e-53 220.0
35 TraesCS4B01G384000 chr2B 90.361 166 16 0 347 512 539366818 539366983 5.350000e-53 219.0
36 TraesCS4B01G384000 chr2D 88.764 178 16 4 341 516 33734744 33734919 6.920000e-52 215.0
37 TraesCS4B01G384000 chr2D 88.764 178 16 4 341 516 33735064 33735239 6.920000e-52 215.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4B01G384000 chr4B 663519703 663522889 3186 False 5886.000000 5886 100.000000 1 3187 1 chr4B.!!$F3 3186
1 TraesCS4B01G384000 chr4B 663461548 663465055 3507 False 902.475000 2527 92.418500 49 3187 4 chr4B.!!$F5 3138
2 TraesCS4B01G384000 chr4B 663621134 663622195 1061 False 798.000000 1437 95.217500 1 1581 2 chr4B.!!$F6 1580
3 TraesCS4B01G384000 chr4B 662713905 662721133 7228 True 555.100000 2532 94.046714 49 3187 7 chr4B.!!$R1 3138
4 TraesCS4B01G384000 chr4B 663627475 663630016 2541 False 453.266667 1142 96.612000 1577 2339 3 chr4B.!!$F7 762

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
113 115 0.455005 CGAACTACTCCCTCCGTTCC 59.545 60.0 0.00 0.0 33.92 3.62 F
116 118 0.702902 ACTACTCCCTCCGTTCCTGA 59.297 55.0 0.00 0.0 0.00 3.86 F
1280 1962 0.741915 ATCTTCTCCGTCGAAGGCTC 59.258 55.0 13.06 0.0 40.56 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1934 4354 0.386476 CCTTGCACCGCCGTAGTATA 59.614 55.0 0.00 0.0 0.0 1.47 R
1995 4415 2.431057 GTGACGTCCCAGAATCTACCAT 59.569 50.0 14.12 0.0 0.0 3.55 R
3143 10004 0.614415 TGTGATCATTGGGGGTTGCC 60.614 55.0 0.00 0.0 0.0 4.52 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
86 87 6.566197 AAAGTAGAAAGAAAGATGCACCAG 57.434 37.500 0.00 0.00 0.00 4.00
99 101 1.411246 TGCACCAGAGTGTTACGAACT 59.589 47.619 0.00 0.00 46.35 3.01
100 102 2.624364 TGCACCAGAGTGTTACGAACTA 59.376 45.455 0.00 0.00 46.35 2.24
101 103 2.985139 GCACCAGAGTGTTACGAACTAC 59.015 50.000 0.00 0.00 46.35 2.73
102 104 3.305199 GCACCAGAGTGTTACGAACTACT 60.305 47.826 0.00 0.00 46.35 2.57
103 105 4.474113 CACCAGAGTGTTACGAACTACTC 58.526 47.826 14.61 14.61 39.30 2.59
104 106 3.505293 ACCAGAGTGTTACGAACTACTCC 59.495 47.826 16.59 7.87 38.84 3.85
105 107 3.119566 CCAGAGTGTTACGAACTACTCCC 60.120 52.174 16.59 5.14 38.84 4.30
106 108 3.757493 CAGAGTGTTACGAACTACTCCCT 59.243 47.826 16.59 0.00 38.84 4.20
107 109 4.009002 AGAGTGTTACGAACTACTCCCTC 58.991 47.826 16.59 0.00 38.84 4.30
108 110 3.087781 AGTGTTACGAACTACTCCCTCC 58.912 50.000 0.00 0.00 0.00 4.30
109 111 2.086869 TGTTACGAACTACTCCCTCCG 58.913 52.381 0.00 0.00 0.00 4.63
110 112 2.087646 GTTACGAACTACTCCCTCCGT 58.912 52.381 0.00 0.00 0.00 4.69
111 113 2.489722 GTTACGAACTACTCCCTCCGTT 59.510 50.000 0.00 0.00 0.00 4.44
112 114 1.172175 ACGAACTACTCCCTCCGTTC 58.828 55.000 0.00 0.00 34.07 3.95
113 115 0.455005 CGAACTACTCCCTCCGTTCC 59.545 60.000 0.00 0.00 33.92 3.62
114 116 1.849977 GAACTACTCCCTCCGTTCCT 58.150 55.000 0.00 0.00 31.89 3.36
115 117 1.477295 GAACTACTCCCTCCGTTCCTG 59.523 57.143 0.00 0.00 31.89 3.86
116 118 0.702902 ACTACTCCCTCCGTTCCTGA 59.297 55.000 0.00 0.00 0.00 3.86
117 119 1.076677 ACTACTCCCTCCGTTCCTGAA 59.923 52.381 0.00 0.00 0.00 3.02
118 120 2.292323 ACTACTCCCTCCGTTCCTGAAT 60.292 50.000 0.00 0.00 0.00 2.57
119 121 2.544844 ACTCCCTCCGTTCCTGAATA 57.455 50.000 0.00 0.00 0.00 1.75
120 122 2.829023 ACTCCCTCCGTTCCTGAATAA 58.171 47.619 0.00 0.00 0.00 1.40
121 123 3.385115 ACTCCCTCCGTTCCTGAATAAT 58.615 45.455 0.00 0.00 0.00 1.28
122 124 3.780850 ACTCCCTCCGTTCCTGAATAATT 59.219 43.478 0.00 0.00 0.00 1.40
123 125 4.130118 CTCCCTCCGTTCCTGAATAATTG 58.870 47.826 0.00 0.00 0.00 2.32
124 126 3.521937 TCCCTCCGTTCCTGAATAATTGT 59.478 43.478 0.00 0.00 0.00 2.71
125 127 3.877508 CCCTCCGTTCCTGAATAATTGTC 59.122 47.826 0.00 0.00 0.00 3.18
126 128 4.384208 CCCTCCGTTCCTGAATAATTGTCT 60.384 45.833 0.00 0.00 0.00 3.41
127 129 5.186198 CCTCCGTTCCTGAATAATTGTCTT 58.814 41.667 0.00 0.00 0.00 3.01
128 130 5.648092 CCTCCGTTCCTGAATAATTGTCTTT 59.352 40.000 0.00 0.00 0.00 2.52
129 131 6.183360 CCTCCGTTCCTGAATAATTGTCTTTC 60.183 42.308 0.00 0.00 0.00 2.62
130 132 6.472887 TCCGTTCCTGAATAATTGTCTTTCT 58.527 36.000 0.00 0.00 0.00 2.52
131 133 7.617225 TCCGTTCCTGAATAATTGTCTTTCTA 58.383 34.615 0.00 0.00 0.00 2.10
132 134 7.764443 TCCGTTCCTGAATAATTGTCTTTCTAG 59.236 37.037 0.00 0.00 0.00 2.43
133 135 7.764443 CCGTTCCTGAATAATTGTCTTTCTAGA 59.236 37.037 0.00 0.00 0.00 2.43
134 136 9.151471 CGTTCCTGAATAATTGTCTTTCTAGAA 57.849 33.333 0.00 0.00 30.65 2.10
181 183 9.436957 ACGAAGTAAAATGAATGAATCTACACT 57.563 29.630 0.00 0.00 41.94 3.55
182 184 9.907576 CGAAGTAAAATGAATGAATCTACACTC 57.092 33.333 0.00 0.00 0.00 3.51
192 194 9.725019 TGAATGAATCTACACTCTAAAACATGT 57.275 29.630 0.00 0.00 0.00 3.21
194 196 9.950496 AATGAATCTACACTCTAAAACATGTCT 57.050 29.630 0.00 0.00 0.00 3.41
196 198 9.856488 TGAATCTACACTCTAAAACATGTCTAC 57.144 33.333 0.00 0.00 0.00 2.59
197 199 9.856488 GAATCTACACTCTAAAACATGTCTACA 57.144 33.333 0.00 0.00 0.00 2.74
203 205 9.587772 ACACTCTAAAACATGTCTACATACATC 57.412 33.333 0.00 0.00 38.01 3.06
204 206 9.035607 CACTCTAAAACATGTCTACATACATCC 57.964 37.037 0.00 0.00 38.01 3.51
205 207 7.921214 ACTCTAAAACATGTCTACATACATCCG 59.079 37.037 0.00 0.00 38.01 4.18
206 208 7.778083 TCTAAAACATGTCTACATACATCCGT 58.222 34.615 0.00 0.00 38.01 4.69
207 209 8.905850 TCTAAAACATGTCTACATACATCCGTA 58.094 33.333 0.00 0.00 38.01 4.02
208 210 9.692749 CTAAAACATGTCTACATACATCCGTAT 57.307 33.333 0.00 0.00 38.01 3.06
222 224 9.653287 CATACATCCGTATGTTTATAGTCCATT 57.347 33.333 0.00 0.00 46.70 3.16
224 226 8.378172 ACATCCGTATGTTTATAGTCCATTTG 57.622 34.615 0.00 0.00 44.07 2.32
225 227 8.208224 ACATCCGTATGTTTATAGTCCATTTGA 58.792 33.333 0.00 0.00 44.07 2.69
226 228 8.712363 CATCCGTATGTTTATAGTCCATTTGAG 58.288 37.037 0.00 0.00 0.00 3.02
227 229 8.014070 TCCGTATGTTTATAGTCCATTTGAGA 57.986 34.615 0.00 0.00 0.00 3.27
228 230 8.647796 TCCGTATGTTTATAGTCCATTTGAGAT 58.352 33.333 0.00 0.00 0.00 2.75
229 231 8.712363 CCGTATGTTTATAGTCCATTTGAGATG 58.288 37.037 0.00 0.00 0.00 2.90
230 232 8.712363 CGTATGTTTATAGTCCATTTGAGATGG 58.288 37.037 0.00 0.00 40.48 3.51
231 233 6.942532 TGTTTATAGTCCATTTGAGATGGC 57.057 37.500 0.00 0.00 39.01 4.40
232 234 6.662755 TGTTTATAGTCCATTTGAGATGGCT 58.337 36.000 0.00 1.24 39.01 4.75
233 235 7.801104 TGTTTATAGTCCATTTGAGATGGCTA 58.199 34.615 0.00 3.36 39.01 3.93
234 236 7.933577 TGTTTATAGTCCATTTGAGATGGCTAG 59.066 37.037 0.00 0.00 39.01 3.42
235 237 7.855784 TTATAGTCCATTTGAGATGGCTAGA 57.144 36.000 0.00 0.00 39.01 2.43
236 238 6.753913 ATAGTCCATTTGAGATGGCTAGAA 57.246 37.500 0.00 0.00 39.01 2.10
237 239 5.441718 AGTCCATTTGAGATGGCTAGAAA 57.558 39.130 0.00 0.00 39.01 2.52
238 240 5.435291 AGTCCATTTGAGATGGCTAGAAAG 58.565 41.667 0.00 0.00 39.01 2.62
239 241 5.190528 AGTCCATTTGAGATGGCTAGAAAGA 59.809 40.000 0.00 0.00 39.01 2.52
240 242 6.060788 GTCCATTTGAGATGGCTAGAAAGAT 58.939 40.000 0.00 0.00 39.01 2.40
241 243 7.071698 AGTCCATTTGAGATGGCTAGAAAGATA 59.928 37.037 0.00 0.00 39.01 1.98
242 244 7.716998 GTCCATTTGAGATGGCTAGAAAGATAA 59.283 37.037 0.00 0.00 39.01 1.75
243 245 8.443176 TCCATTTGAGATGGCTAGAAAGATAAT 58.557 33.333 0.00 0.00 39.01 1.28
244 246 9.075678 CCATTTGAGATGGCTAGAAAGATAATT 57.924 33.333 0.00 0.00 31.75 1.40
259 261 9.331282 AGAAAGATAATTATTTGAGAACCGAGG 57.669 33.333 0.00 0.00 0.00 4.63
260 262 8.451908 AAAGATAATTATTTGAGAACCGAGGG 57.548 34.615 0.00 0.00 0.00 4.30
261 263 7.374975 AGATAATTATTTGAGAACCGAGGGA 57.625 36.000 0.00 0.00 0.00 4.20
262 264 7.445945 AGATAATTATTTGAGAACCGAGGGAG 58.554 38.462 0.00 0.00 0.00 4.30
324 326 1.204941 AGACAGAACGGCTAATTCGCT 59.795 47.619 1.63 0.00 0.00 4.93
333 335 8.162880 CAGAACGGCTAATTCGCTAATATAAAG 58.837 37.037 1.63 0.00 0.00 1.85
357 359 7.288560 AGAATTACTATTCACTACTCCCTCGA 58.711 38.462 0.00 0.00 42.18 4.04
358 360 7.945664 AGAATTACTATTCACTACTCCCTCGAT 59.054 37.037 0.00 0.00 42.18 3.59
359 361 8.480133 AATTACTATTCACTACTCCCTCGATT 57.520 34.615 0.00 0.00 0.00 3.34
360 362 7.507733 TTACTATTCACTACTCCCTCGATTC 57.492 40.000 0.00 0.00 0.00 2.52
362 364 3.383698 TTCACTACTCCCTCGATTCCT 57.616 47.619 0.00 0.00 0.00 3.36
363 365 4.515028 TTCACTACTCCCTCGATTCCTA 57.485 45.455 0.00 0.00 0.00 2.94
364 366 4.515028 TCACTACTCCCTCGATTCCTAA 57.485 45.455 0.00 0.00 0.00 2.69
365 367 4.863548 TCACTACTCCCTCGATTCCTAAA 58.136 43.478 0.00 0.00 0.00 1.85
366 368 5.455872 TCACTACTCCCTCGATTCCTAAAT 58.544 41.667 0.00 0.00 0.00 1.40
367 369 6.607970 TCACTACTCCCTCGATTCCTAAATA 58.392 40.000 0.00 0.00 0.00 1.40
368 370 7.239438 TCACTACTCCCTCGATTCCTAAATAT 58.761 38.462 0.00 0.00 0.00 1.28
369 371 8.388589 TCACTACTCCCTCGATTCCTAAATATA 58.611 37.037 0.00 0.00 0.00 0.86
370 372 9.021807 CACTACTCCCTCGATTCCTAAATATAA 57.978 37.037 0.00 0.00 0.00 0.98
371 373 9.245481 ACTACTCCCTCGATTCCTAAATATAAG 57.755 37.037 0.00 0.00 0.00 1.73
372 374 9.245481 CTACTCCCTCGATTCCTAAATATAAGT 57.755 37.037 0.00 0.00 0.00 2.24
373 375 8.493787 ACTCCCTCGATTCCTAAATATAAGTT 57.506 34.615 0.00 0.00 0.00 2.66
374 376 8.935741 ACTCCCTCGATTCCTAAATATAAGTTT 58.064 33.333 0.00 0.00 0.00 2.66
375 377 9.780186 CTCCCTCGATTCCTAAATATAAGTTTT 57.220 33.333 0.00 0.00 0.00 2.43
405 407 1.686587 TCCACTATGGAGCACATACGG 59.313 52.381 0.00 2.66 42.67 4.02
406 408 1.686587 CCACTATGGAGCACATACGGA 59.313 52.381 0.00 0.00 40.96 4.69
407 409 2.288457 CCACTATGGAGCACATACGGAG 60.288 54.545 0.00 0.00 40.96 4.63
408 410 4.810531 CCACTATGGAGCACATACGGAGT 61.811 52.174 0.00 0.00 42.93 3.85
409 411 5.525987 CCACTATGGAGCACATACGGAGTA 61.526 50.000 0.00 0.00 44.55 2.59
410 412 6.954903 CCACTATGGAGCACATACGGAGTAA 61.955 48.000 0.00 0.00 43.87 2.24
411 413 8.351111 CCACTATGGAGCACATACGGAGTAAA 62.351 46.154 0.00 0.00 43.87 2.01
412 414 9.718215 CCACTATGGAGCACATACGGAGTAAAA 62.718 44.444 0.00 0.00 43.87 1.52
426 428 7.360575 ACGGAGTAAAATGAATGAACTACAC 57.639 36.000 0.00 0.00 41.94 2.90
427 429 7.159372 ACGGAGTAAAATGAATGAACTACACT 58.841 34.615 0.00 0.00 41.94 3.55
428 430 7.331193 ACGGAGTAAAATGAATGAACTACACTC 59.669 37.037 0.00 0.00 41.94 3.51
429 431 7.201530 CGGAGTAAAATGAATGAACTACACTCC 60.202 40.741 0.00 0.00 43.09 3.85
430 432 7.606456 GGAGTAAAATGAATGAACTACACTCCA 59.394 37.037 0.00 0.00 44.93 3.86
431 433 8.918202 AGTAAAATGAATGAACTACACTCCAA 57.082 30.769 0.00 0.00 0.00 3.53
432 434 9.349713 AGTAAAATGAATGAACTACACTCCAAA 57.650 29.630 0.00 0.00 0.00 3.28
433 435 9.959749 GTAAAATGAATGAACTACACTCCAAAA 57.040 29.630 0.00 0.00 0.00 2.44
435 437 9.480053 AAAATGAATGAACTACACTCCAAAATG 57.520 29.630 0.00 0.00 0.00 2.32
436 438 6.012658 TGAATGAACTACACTCCAAAATGC 57.987 37.500 0.00 0.00 0.00 3.56
437 439 5.534278 TGAATGAACTACACTCCAAAATGCA 59.466 36.000 0.00 0.00 0.00 3.96
438 440 6.209192 TGAATGAACTACACTCCAAAATGCAT 59.791 34.615 0.00 0.00 0.00 3.96
439 441 5.627499 TGAACTACACTCCAAAATGCATC 57.373 39.130 0.00 0.00 0.00 3.91
440 442 5.316167 TGAACTACACTCCAAAATGCATCT 58.684 37.500 0.00 0.00 0.00 2.90
441 443 6.472016 TGAACTACACTCCAAAATGCATCTA 58.528 36.000 0.00 0.00 0.00 1.98
442 444 7.112122 TGAACTACACTCCAAAATGCATCTAT 58.888 34.615 0.00 0.00 0.00 1.98
443 445 8.264347 TGAACTACACTCCAAAATGCATCTATA 58.736 33.333 0.00 0.00 0.00 1.31
444 446 9.277783 GAACTACACTCCAAAATGCATCTATAT 57.722 33.333 0.00 0.00 0.00 0.86
446 448 9.712305 ACTACACTCCAAAATGCATCTATATAC 57.288 33.333 0.00 0.00 0.00 1.47
447 449 9.710900 CTACACTCCAAAATGCATCTATATACA 57.289 33.333 0.00 0.00 0.00 2.29
449 451 9.224267 ACACTCCAAAATGCATCTATATACATC 57.776 33.333 0.00 0.00 0.00 3.06
450 452 8.671921 CACTCCAAAATGCATCTATATACATCC 58.328 37.037 0.00 0.00 0.00 3.51
451 453 7.550551 ACTCCAAAATGCATCTATATACATCCG 59.449 37.037 0.00 0.00 0.00 4.18
452 454 7.394016 TCCAAAATGCATCTATATACATCCGT 58.606 34.615 0.00 0.00 0.00 4.69
453 455 8.536175 TCCAAAATGCATCTATATACATCCGTA 58.464 33.333 0.00 0.00 0.00 4.02
454 456 9.330063 CCAAAATGCATCTATATACATCCGTAT 57.670 33.333 0.00 0.00 41.34 3.06
457 459 8.877808 AATGCATCTATATACATCCGTATGTG 57.122 34.615 3.56 0.00 45.99 3.21
458 460 6.805713 TGCATCTATATACATCCGTATGTGG 58.194 40.000 3.56 0.00 45.99 4.17
459 461 6.379988 TGCATCTATATACATCCGTATGTGGT 59.620 38.462 3.56 0.00 45.99 4.16
460 462 7.093509 TGCATCTATATACATCCGTATGTGGTT 60.094 37.037 3.56 0.00 45.99 3.67
461 463 7.764443 GCATCTATATACATCCGTATGTGGTTT 59.236 37.037 3.56 0.00 45.99 3.27
468 470 6.474140 ACATCCGTATGTGGTTTATAGTGA 57.526 37.500 0.00 0.00 44.79 3.41
469 471 6.880484 ACATCCGTATGTGGTTTATAGTGAA 58.120 36.000 0.00 0.00 44.79 3.18
470 472 7.332557 ACATCCGTATGTGGTTTATAGTGAAA 58.667 34.615 0.00 0.00 44.79 2.69
471 473 7.990886 ACATCCGTATGTGGTTTATAGTGAAAT 59.009 33.333 0.00 0.00 44.79 2.17
472 474 8.495949 CATCCGTATGTGGTTTATAGTGAAATC 58.504 37.037 0.00 0.00 0.00 2.17
473 475 7.788026 TCCGTATGTGGTTTATAGTGAAATCT 58.212 34.615 0.00 0.00 0.00 2.40
474 476 8.916062 TCCGTATGTGGTTTATAGTGAAATCTA 58.084 33.333 0.00 0.00 0.00 1.98
475 477 9.706691 CCGTATGTGGTTTATAGTGAAATCTAT 57.293 33.333 0.00 0.00 35.24 1.98
503 505 8.707796 ATAGACTTATATTTGAGAACGGAGGA 57.292 34.615 0.00 0.00 0.00 3.71
504 506 7.419711 AGACTTATATTTGAGAACGGAGGAA 57.580 36.000 0.00 0.00 0.00 3.36
505 507 7.493367 AGACTTATATTTGAGAACGGAGGAAG 58.507 38.462 0.00 0.00 0.00 3.46
506 508 7.124448 AGACTTATATTTGAGAACGGAGGAAGT 59.876 37.037 0.00 0.00 0.00 3.01
507 509 8.302515 ACTTATATTTGAGAACGGAGGAAGTA 57.697 34.615 0.00 0.00 0.00 2.24
508 510 8.925338 ACTTATATTTGAGAACGGAGGAAGTAT 58.075 33.333 0.00 0.00 0.00 2.12
509 511 9.765795 CTTATATTTGAGAACGGAGGAAGTATT 57.234 33.333 0.00 0.00 0.00 1.89
521 523 7.116736 ACGGAGGAAGTATTAATTCAATGGTT 58.883 34.615 6.25 0.00 0.00 3.67
531 533 2.483583 TTCAATGGTTTCACGTGCAC 57.516 45.000 11.67 6.82 0.00 4.57
552 554 6.866248 TGCACGAAAAAGAAAGAGAAAAGTTT 59.134 30.769 0.00 0.00 0.00 2.66
571 573 9.705290 AAAAGTTTGGTCATACATTAATTGGAC 57.295 29.630 0.00 0.00 0.00 4.02
588 590 3.693807 TGGACGAGAGAGGCTACTAAAA 58.306 45.455 0.00 0.00 0.00 1.52
657 660 5.957771 ACATTTAGATAGAGTCCAGGCAA 57.042 39.130 0.00 0.00 0.00 4.52
667 670 3.575687 AGAGTCCAGGCAAAAATGGAAAG 59.424 43.478 0.00 0.00 46.87 2.62
672 675 5.588246 GTCCAGGCAAAAATGGAAAGAAAAA 59.412 36.000 0.00 0.00 46.87 1.94
725 1397 0.817654 TGCATGTAGACGGACTCCAG 59.182 55.000 0.00 0.00 0.00 3.86
890 1572 2.567169 GCTTTGTTGGCCTCCCTAATTT 59.433 45.455 3.32 0.00 0.00 1.82
936 1618 6.126478 CCACTAATTTTCAATCCTCCCTCCTA 60.126 42.308 0.00 0.00 0.00 2.94
1280 1962 0.741915 ATCTTCTCCGTCGAAGGCTC 59.258 55.000 13.06 0.00 40.56 4.70
1309 1991 1.741770 GCCGGGTACAAGCTCACTG 60.742 63.158 2.18 0.00 0.00 3.66
1370 2052 1.426251 AACCTGTCTCCCATGGTGCA 61.426 55.000 11.73 2.97 32.53 4.57
1608 4028 1.614241 TTAAGGGGGTGAGCTCGCTC 61.614 60.000 25.54 22.62 37.40 5.03
1995 4415 4.380531 GAAGGTGATAATCTTCGATGGCA 58.619 43.478 0.00 0.00 31.51 4.92
2069 4489 4.808414 ATTCGATATCGTGATGATGGGT 57.192 40.909 23.61 0.00 37.99 4.51
2236 4656 6.040166 GGTTCGTCTACTATTGAATCCTACCA 59.960 42.308 0.00 0.00 0.00 3.25
2363 4828 8.243426 CGAGATTTTCATCCTTTGTTCCATAAA 58.757 33.333 0.00 0.00 0.00 1.40
2372 5410 6.318913 TCCTTTGTTCCATAAAGATTCCCAA 58.681 36.000 0.00 0.00 37.33 4.12
2400 5438 2.642139 ATGCTTTCATGCTTTGGTCG 57.358 45.000 0.00 0.00 0.00 4.79
2459 9059 2.618219 CCGAGCTCTACCCGATCGG 61.618 68.421 27.65 27.65 45.95 4.18
2505 9132 3.719268 AATGTCTCCACCTTATGTGCA 57.281 42.857 0.00 0.00 44.01 4.57
2560 9187 5.811399 TTATTATTTCAGTTGTCCTGCCG 57.189 39.130 0.00 0.00 41.25 5.69
2561 9188 2.851263 TATTTCAGTTGTCCTGCCGT 57.149 45.000 0.00 0.00 41.25 5.68
2562 9189 1.981256 ATTTCAGTTGTCCTGCCGTT 58.019 45.000 0.00 0.00 41.25 4.44
2611 9238 3.622060 ATCGCCGGGACCAACAAGG 62.622 63.158 2.18 0.00 45.67 3.61
2626 9253 0.824109 CAAGGTACTGCAGATCGGGA 59.176 55.000 23.35 0.00 40.86 5.14
2635 9262 1.148157 GCAGATCGGGACATCACACG 61.148 60.000 0.00 0.00 38.09 4.49
2711 9338 1.442769 GATGAGCCGTGAACACACAT 58.557 50.000 5.80 5.12 34.59 3.21
2744 9371 0.943673 CATGTGCGACACTGGAAACA 59.056 50.000 10.54 0.00 35.11 2.83
2797 9424 7.970061 GTGTGCTAAATTGATGTTGTCACATAT 59.030 33.333 0.00 0.00 44.22 1.78
2798 9425 9.171877 TGTGCTAAATTGATGTTGTCACATATA 57.828 29.630 0.00 0.00 44.22 0.86
2799 9426 9.438291 GTGCTAAATTGATGTTGTCACATATAC 57.562 33.333 0.00 0.00 44.22 1.47
2800 9427 8.334632 TGCTAAATTGATGTTGTCACATATACG 58.665 33.333 0.00 0.00 44.22 3.06
2801 9428 8.547894 GCTAAATTGATGTTGTCACATATACGA 58.452 33.333 0.00 0.00 44.22 3.43
3070 9931 1.965643 GGTAACCCCCAAAACTTGACC 59.034 52.381 0.00 0.00 0.00 4.02
3115 9976 3.016541 GCGCCAATGCCCAAATCCA 62.017 57.895 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 1.267334 CCGTACATTTTGCCGATCACG 60.267 52.381 0.00 0.00 39.43 4.35
86 87 3.128415 GGAGGGAGTAGTTCGTAACACTC 59.872 52.174 14.35 14.35 38.09 3.51
99 101 2.544844 ATTCAGGAACGGAGGGAGTA 57.455 50.000 0.00 0.00 31.97 2.59
100 102 2.544844 TATTCAGGAACGGAGGGAGT 57.455 50.000 0.00 0.00 31.97 3.85
101 103 4.130118 CAATTATTCAGGAACGGAGGGAG 58.870 47.826 0.00 0.00 31.97 4.30
102 104 3.521937 ACAATTATTCAGGAACGGAGGGA 59.478 43.478 0.00 0.00 31.97 4.20
103 105 3.877508 GACAATTATTCAGGAACGGAGGG 59.122 47.826 0.00 0.00 31.97 4.30
104 106 4.770795 AGACAATTATTCAGGAACGGAGG 58.229 43.478 0.00 0.00 31.97 4.30
105 107 6.595716 AGAAAGACAATTATTCAGGAACGGAG 59.404 38.462 0.00 0.00 31.97 4.63
106 108 6.472887 AGAAAGACAATTATTCAGGAACGGA 58.527 36.000 0.00 0.00 0.00 4.69
107 109 6.743575 AGAAAGACAATTATTCAGGAACGG 57.256 37.500 0.00 0.00 0.00 4.44
108 110 8.703604 TCTAGAAAGACAATTATTCAGGAACG 57.296 34.615 0.00 0.00 0.00 3.95
135 137 9.485206 ACTTCGTATGTAGTTACTTGTTGAAAT 57.515 29.630 0.00 0.00 0.00 2.17
136 138 8.876275 ACTTCGTATGTAGTTACTTGTTGAAA 57.124 30.769 0.00 0.00 0.00 2.69
137 139 9.964303 TTACTTCGTATGTAGTTACTTGTTGAA 57.036 29.630 0.00 0.00 0.00 2.69
138 140 9.964303 TTTACTTCGTATGTAGTTACTTGTTGA 57.036 29.630 0.00 0.00 0.00 3.18
155 157 9.436957 AGTGTAGATTCATTCATTTTACTTCGT 57.563 29.630 0.00 0.00 0.00 3.85
156 158 9.907576 GAGTGTAGATTCATTCATTTTACTTCG 57.092 33.333 0.00 0.00 0.00 3.79
166 168 9.725019 ACATGTTTTAGAGTGTAGATTCATTCA 57.275 29.630 0.00 0.00 0.00 2.57
168 170 9.950496 AGACATGTTTTAGAGTGTAGATTCATT 57.050 29.630 0.00 0.00 0.00 2.57
170 172 9.856488 GTAGACATGTTTTAGAGTGTAGATTCA 57.144 33.333 0.00 0.00 0.00 2.57
171 173 9.856488 TGTAGACATGTTTTAGAGTGTAGATTC 57.144 33.333 0.00 0.00 0.00 2.52
177 179 9.587772 GATGTATGTAGACATGTTTTAGAGTGT 57.412 33.333 0.00 0.00 40.18 3.55
178 180 9.035607 GGATGTATGTAGACATGTTTTAGAGTG 57.964 37.037 0.00 0.00 40.18 3.51
179 181 7.921214 CGGATGTATGTAGACATGTTTTAGAGT 59.079 37.037 0.00 0.00 40.18 3.24
180 182 7.921214 ACGGATGTATGTAGACATGTTTTAGAG 59.079 37.037 0.00 0.00 40.18 2.43
181 183 7.778083 ACGGATGTATGTAGACATGTTTTAGA 58.222 34.615 0.00 0.00 40.18 2.10
182 184 9.692749 ATACGGATGTATGTAGACATGTTTTAG 57.307 33.333 0.00 0.00 40.18 1.85
198 200 9.483916 CAAATGGACTATAAACATACGGATGTA 57.516 33.333 15.10 0.00 45.93 2.29
200 202 8.601845 TCAAATGGACTATAAACATACGGATG 57.398 34.615 5.94 5.94 39.16 3.51
201 203 8.647796 TCTCAAATGGACTATAAACATACGGAT 58.352 33.333 0.00 0.00 0.00 4.18
202 204 8.014070 TCTCAAATGGACTATAAACATACGGA 57.986 34.615 0.00 0.00 0.00 4.69
203 205 8.712363 CATCTCAAATGGACTATAAACATACGG 58.288 37.037 0.00 0.00 0.00 4.02
204 206 8.712363 CCATCTCAAATGGACTATAAACATACG 58.288 37.037 0.00 0.00 41.64 3.06
205 207 8.507249 GCCATCTCAAATGGACTATAAACATAC 58.493 37.037 8.23 0.00 41.64 2.39
206 208 8.439971 AGCCATCTCAAATGGACTATAAACATA 58.560 33.333 8.23 0.00 41.64 2.29
207 209 7.293073 AGCCATCTCAAATGGACTATAAACAT 58.707 34.615 8.23 0.00 41.64 2.71
208 210 6.662755 AGCCATCTCAAATGGACTATAAACA 58.337 36.000 8.23 0.00 41.64 2.83
209 211 8.150945 TCTAGCCATCTCAAATGGACTATAAAC 58.849 37.037 8.23 0.00 41.64 2.01
210 212 8.262601 TCTAGCCATCTCAAATGGACTATAAA 57.737 34.615 8.23 0.00 41.64 1.40
211 213 7.855784 TCTAGCCATCTCAAATGGACTATAA 57.144 36.000 8.23 0.00 41.64 0.98
212 214 7.855784 TTCTAGCCATCTCAAATGGACTATA 57.144 36.000 8.23 0.55 41.64 1.31
213 215 6.753913 TTCTAGCCATCTCAAATGGACTAT 57.246 37.500 8.23 0.00 41.64 2.12
214 216 6.384015 TCTTTCTAGCCATCTCAAATGGACTA 59.616 38.462 8.23 7.79 41.64 2.59
215 217 5.190528 TCTTTCTAGCCATCTCAAATGGACT 59.809 40.000 8.23 7.12 41.64 3.85
216 218 5.431765 TCTTTCTAGCCATCTCAAATGGAC 58.568 41.667 8.23 0.19 41.64 4.02
217 219 5.698741 TCTTTCTAGCCATCTCAAATGGA 57.301 39.130 8.23 0.00 41.64 3.41
218 220 8.632906 ATTATCTTTCTAGCCATCTCAAATGG 57.367 34.615 0.00 0.00 41.99 3.16
233 235 9.331282 CCTCGGTTCTCAAATAATTATCTTTCT 57.669 33.333 0.00 0.00 0.00 2.52
234 236 8.560374 CCCTCGGTTCTCAAATAATTATCTTTC 58.440 37.037 0.00 0.00 0.00 2.62
235 237 8.272173 TCCCTCGGTTCTCAAATAATTATCTTT 58.728 33.333 0.00 0.00 0.00 2.52
236 238 7.802117 TCCCTCGGTTCTCAAATAATTATCTT 58.198 34.615 0.00 0.00 0.00 2.40
237 239 7.071321 ACTCCCTCGGTTCTCAAATAATTATCT 59.929 37.037 0.00 0.00 0.00 1.98
238 240 7.217906 ACTCCCTCGGTTCTCAAATAATTATC 58.782 38.462 0.00 0.00 0.00 1.75
239 241 7.138054 ACTCCCTCGGTTCTCAAATAATTAT 57.862 36.000 0.00 0.00 0.00 1.28
240 242 6.555463 ACTCCCTCGGTTCTCAAATAATTA 57.445 37.500 0.00 0.00 0.00 1.40
241 243 5.437191 ACTCCCTCGGTTCTCAAATAATT 57.563 39.130 0.00 0.00 0.00 1.40
242 244 5.897824 TCTACTCCCTCGGTTCTCAAATAAT 59.102 40.000 0.00 0.00 0.00 1.28
243 245 5.266788 TCTACTCCCTCGGTTCTCAAATAA 58.733 41.667 0.00 0.00 0.00 1.40
244 246 4.863548 TCTACTCCCTCGGTTCTCAAATA 58.136 43.478 0.00 0.00 0.00 1.40
245 247 3.709587 TCTACTCCCTCGGTTCTCAAAT 58.290 45.455 0.00 0.00 0.00 2.32
246 248 3.165087 TCTACTCCCTCGGTTCTCAAA 57.835 47.619 0.00 0.00 0.00 2.69
247 249 2.824341 GTTCTACTCCCTCGGTTCTCAA 59.176 50.000 0.00 0.00 0.00 3.02
248 250 2.041350 AGTTCTACTCCCTCGGTTCTCA 59.959 50.000 0.00 0.00 0.00 3.27
249 251 2.725637 AGTTCTACTCCCTCGGTTCTC 58.274 52.381 0.00 0.00 0.00 2.87
250 252 2.903375 AGTTCTACTCCCTCGGTTCT 57.097 50.000 0.00 0.00 0.00 3.01
251 253 2.358582 GCTAGTTCTACTCCCTCGGTTC 59.641 54.545 0.00 0.00 0.00 3.62
252 254 2.025131 AGCTAGTTCTACTCCCTCGGTT 60.025 50.000 0.00 0.00 0.00 4.44
253 255 1.565288 AGCTAGTTCTACTCCCTCGGT 59.435 52.381 0.00 0.00 0.00 4.69
254 256 2.351706 AGCTAGTTCTACTCCCTCGG 57.648 55.000 0.00 0.00 0.00 4.63
255 257 4.075963 AGTAGCTAGTTCTACTCCCTCG 57.924 50.000 0.00 0.00 44.22 4.63
262 264 6.207221 GGGAATAGTGGAGTAGCTAGTTCTAC 59.793 46.154 8.37 10.22 39.28 2.59
283 285 9.137459 CTGTCTTATAATCTCTAACAGAGGGAA 57.863 37.037 3.47 0.00 42.54 3.97
333 335 7.507733 TCGAGGGAGTAGTGAATAGTAATTC 57.492 40.000 0.00 0.00 41.69 2.17
349 351 9.780186 AAAACTTATATTTAGGAATCGAGGGAG 57.220 33.333 0.00 0.00 0.00 4.30
385 387 1.686587 CCGTATGTGCTCCATAGTGGA 59.313 52.381 0.00 0.00 45.98 4.02
386 388 1.686587 TCCGTATGTGCTCCATAGTGG 59.313 52.381 7.98 7.98 36.71 4.00
387 389 2.362397 ACTCCGTATGTGCTCCATAGTG 59.638 50.000 0.00 0.00 36.71 2.74
388 390 2.667470 ACTCCGTATGTGCTCCATAGT 58.333 47.619 0.00 0.00 36.71 2.12
389 391 4.848562 TTACTCCGTATGTGCTCCATAG 57.151 45.455 0.00 0.00 36.71 2.23
390 392 5.601583 TTTTACTCCGTATGTGCTCCATA 57.398 39.130 0.00 0.00 34.86 2.74
391 393 4.481368 TTTTACTCCGTATGTGCTCCAT 57.519 40.909 0.00 0.00 37.58 3.41
392 394 3.965379 TTTTACTCCGTATGTGCTCCA 57.035 42.857 0.00 0.00 0.00 3.86
393 395 4.439057 TCATTTTACTCCGTATGTGCTCC 58.561 43.478 0.00 0.00 0.00 4.70
394 396 6.257849 TCATTCATTTTACTCCGTATGTGCTC 59.742 38.462 0.00 0.00 0.00 4.26
395 397 6.112734 TCATTCATTTTACTCCGTATGTGCT 58.887 36.000 0.00 0.00 0.00 4.40
396 398 6.358118 TCATTCATTTTACTCCGTATGTGC 57.642 37.500 0.00 0.00 0.00 4.57
397 399 7.974675 AGTTCATTCATTTTACTCCGTATGTG 58.025 34.615 0.00 0.00 0.00 3.21
398 400 9.095065 GTAGTTCATTCATTTTACTCCGTATGT 57.905 33.333 0.00 0.00 0.00 2.29
399 401 9.093970 TGTAGTTCATTCATTTTACTCCGTATG 57.906 33.333 0.00 0.00 0.00 2.39
400 402 9.095065 GTGTAGTTCATTCATTTTACTCCGTAT 57.905 33.333 0.00 0.00 0.00 3.06
401 403 8.308931 AGTGTAGTTCATTCATTTTACTCCGTA 58.691 33.333 0.00 0.00 0.00 4.02
402 404 7.159372 AGTGTAGTTCATTCATTTTACTCCGT 58.841 34.615 0.00 0.00 0.00 4.69
403 405 7.201530 GGAGTGTAGTTCATTCATTTTACTCCG 60.202 40.741 0.00 0.00 40.48 4.63
404 406 7.606456 TGGAGTGTAGTTCATTCATTTTACTCC 59.394 37.037 0.00 0.00 46.53 3.85
405 407 8.547967 TGGAGTGTAGTTCATTCATTTTACTC 57.452 34.615 0.00 0.00 34.99 2.59
406 408 8.918202 TTGGAGTGTAGTTCATTCATTTTACT 57.082 30.769 0.00 0.00 34.99 2.24
407 409 9.959749 TTTTGGAGTGTAGTTCATTCATTTTAC 57.040 29.630 0.00 0.00 34.99 2.01
409 411 9.480053 CATTTTGGAGTGTAGTTCATTCATTTT 57.520 29.630 0.00 0.00 34.99 1.82
410 412 7.599998 GCATTTTGGAGTGTAGTTCATTCATTT 59.400 33.333 0.00 0.00 34.99 2.32
411 413 7.092716 GCATTTTGGAGTGTAGTTCATTCATT 58.907 34.615 0.00 0.00 34.99 2.57
412 414 6.209192 TGCATTTTGGAGTGTAGTTCATTCAT 59.791 34.615 0.00 0.00 34.99 2.57
413 415 5.534278 TGCATTTTGGAGTGTAGTTCATTCA 59.466 36.000 0.00 0.00 34.99 2.57
414 416 6.012658 TGCATTTTGGAGTGTAGTTCATTC 57.987 37.500 0.00 0.00 32.96 2.67
415 417 6.435277 AGATGCATTTTGGAGTGTAGTTCATT 59.565 34.615 0.00 0.00 0.00 2.57
416 418 5.948162 AGATGCATTTTGGAGTGTAGTTCAT 59.052 36.000 0.00 0.00 0.00 2.57
417 419 5.316167 AGATGCATTTTGGAGTGTAGTTCA 58.684 37.500 0.00 0.00 0.00 3.18
418 420 5.886960 AGATGCATTTTGGAGTGTAGTTC 57.113 39.130 0.00 0.00 0.00 3.01
420 422 9.712305 GTATATAGATGCATTTTGGAGTGTAGT 57.288 33.333 0.00 0.00 0.00 2.73
421 423 9.710900 TGTATATAGATGCATTTTGGAGTGTAG 57.289 33.333 0.00 0.00 0.00 2.74
423 425 9.224267 GATGTATATAGATGCATTTTGGAGTGT 57.776 33.333 0.00 0.00 38.38 3.55
424 426 8.671921 GGATGTATATAGATGCATTTTGGAGTG 58.328 37.037 0.00 0.00 38.38 3.51
425 427 7.550551 CGGATGTATATAGATGCATTTTGGAGT 59.449 37.037 11.19 0.00 38.38 3.85
426 428 7.550551 ACGGATGTATATAGATGCATTTTGGAG 59.449 37.037 11.19 0.00 38.38 3.86
427 429 7.394016 ACGGATGTATATAGATGCATTTTGGA 58.606 34.615 11.19 0.00 38.38 3.53
428 430 7.615582 ACGGATGTATATAGATGCATTTTGG 57.384 36.000 11.19 0.00 38.38 3.28
430 432 9.890629 ACATACGGATGTATATAGATGCATTTT 57.109 29.630 12.79 0.00 44.77 1.82
431 433 9.317936 CACATACGGATGTATATAGATGCATTT 57.682 33.333 14.23 0.00 44.82 2.32
432 434 7.928167 CCACATACGGATGTATATAGATGCATT 59.072 37.037 14.23 1.23 44.82 3.56
433 435 7.069950 ACCACATACGGATGTATATAGATGCAT 59.930 37.037 14.23 0.00 44.82 3.96
434 436 6.379988 ACCACATACGGATGTATATAGATGCA 59.620 38.462 14.23 0.00 44.82 3.96
435 437 6.806751 ACCACATACGGATGTATATAGATGC 58.193 40.000 14.23 0.00 44.82 3.91
442 444 9.299465 TCACTATAAACCACATACGGATGTATA 57.701 33.333 14.23 6.48 44.82 1.47
443 445 8.185506 TCACTATAAACCACATACGGATGTAT 57.814 34.615 14.23 5.54 44.82 2.29
444 446 7.585579 TCACTATAAACCACATACGGATGTA 57.414 36.000 14.23 0.00 44.82 2.29
446 448 7.780008 TTTCACTATAAACCACATACGGATG 57.220 36.000 5.94 5.94 39.16 3.51
447 449 8.429641 AGATTTCACTATAAACCACATACGGAT 58.570 33.333 0.00 0.00 0.00 4.18
448 450 7.788026 AGATTTCACTATAAACCACATACGGA 58.212 34.615 0.00 0.00 0.00 4.69
449 451 9.706691 ATAGATTTCACTATAAACCACATACGG 57.293 33.333 0.00 0.00 32.21 4.02
477 479 9.803507 TCCTCCGTTCTCAAATATAAGTCTATA 57.196 33.333 0.00 0.00 0.00 1.31
478 480 8.707796 TCCTCCGTTCTCAAATATAAGTCTAT 57.292 34.615 0.00 0.00 0.00 1.98
479 481 8.529424 TTCCTCCGTTCTCAAATATAAGTCTA 57.471 34.615 0.00 0.00 0.00 2.59
480 482 7.124448 ACTTCCTCCGTTCTCAAATATAAGTCT 59.876 37.037 0.00 0.00 0.00 3.24
481 483 7.266400 ACTTCCTCCGTTCTCAAATATAAGTC 58.734 38.462 0.00 0.00 0.00 3.01
482 484 7.184067 ACTTCCTCCGTTCTCAAATATAAGT 57.816 36.000 0.00 0.00 0.00 2.24
483 485 9.765795 AATACTTCCTCCGTTCTCAAATATAAG 57.234 33.333 0.00 0.00 0.00 1.73
488 490 9.110502 GAATTAATACTTCCTCCGTTCTCAAAT 57.889 33.333 0.00 0.00 0.00 2.32
489 491 8.098286 TGAATTAATACTTCCTCCGTTCTCAAA 58.902 33.333 0.00 0.00 0.00 2.69
490 492 7.617225 TGAATTAATACTTCCTCCGTTCTCAA 58.383 34.615 0.00 0.00 0.00 3.02
491 493 7.177832 TGAATTAATACTTCCTCCGTTCTCA 57.822 36.000 0.00 0.00 0.00 3.27
492 494 8.552034 CATTGAATTAATACTTCCTCCGTTCTC 58.448 37.037 0.00 0.00 0.00 2.87
493 495 7.499232 CCATTGAATTAATACTTCCTCCGTTCT 59.501 37.037 0.00 0.00 0.00 3.01
494 496 7.282450 ACCATTGAATTAATACTTCCTCCGTTC 59.718 37.037 0.00 0.00 0.00 3.95
495 497 7.116736 ACCATTGAATTAATACTTCCTCCGTT 58.883 34.615 0.00 0.00 0.00 4.44
496 498 6.659824 ACCATTGAATTAATACTTCCTCCGT 58.340 36.000 0.00 0.00 0.00 4.69
497 499 7.568199 AACCATTGAATTAATACTTCCTCCG 57.432 36.000 0.00 0.00 0.00 4.63
498 500 8.966868 TGAAACCATTGAATTAATACTTCCTCC 58.033 33.333 0.00 0.00 0.00 4.30
499 501 9.788960 GTGAAACCATTGAATTAATACTTCCTC 57.211 33.333 0.00 0.00 0.00 3.71
500 502 8.458843 CGTGAAACCATTGAATTAATACTTCCT 58.541 33.333 0.00 0.00 0.00 3.36
501 503 8.241367 ACGTGAAACCATTGAATTAATACTTCC 58.759 33.333 0.00 0.00 0.00 3.46
502 504 9.061610 CACGTGAAACCATTGAATTAATACTTC 57.938 33.333 10.90 0.00 0.00 3.01
503 505 7.540745 GCACGTGAAACCATTGAATTAATACTT 59.459 33.333 22.23 0.00 0.00 2.24
504 506 7.027161 GCACGTGAAACCATTGAATTAATACT 58.973 34.615 22.23 0.00 0.00 2.12
505 507 6.804295 TGCACGTGAAACCATTGAATTAATAC 59.196 34.615 22.23 0.00 0.00 1.89
506 508 6.804295 GTGCACGTGAAACCATTGAATTAATA 59.196 34.615 22.23 0.00 0.00 0.98
507 509 5.633182 GTGCACGTGAAACCATTGAATTAAT 59.367 36.000 22.23 0.00 0.00 1.40
508 510 4.979197 GTGCACGTGAAACCATTGAATTAA 59.021 37.500 22.23 0.00 0.00 1.40
509 511 4.541779 GTGCACGTGAAACCATTGAATTA 58.458 39.130 22.23 0.00 0.00 1.40
510 512 3.380142 GTGCACGTGAAACCATTGAATT 58.620 40.909 22.23 0.00 0.00 2.17
511 513 2.604373 CGTGCACGTGAAACCATTGAAT 60.604 45.455 30.50 0.00 34.11 2.57
521 523 3.125487 TCTTTCTTTTTCGTGCACGTGAA 59.875 39.130 35.74 27.42 40.80 3.18
531 533 7.540745 TGACCAAACTTTTCTCTTTCTTTTTCG 59.459 33.333 0.00 0.00 0.00 3.46
552 554 6.097696 TCTCTCGTCCAATTAATGTATGACCA 59.902 38.462 0.00 0.00 0.00 4.02
571 573 4.339814 ACATCCTTTTAGTAGCCTCTCTCG 59.660 45.833 0.00 0.00 0.00 4.04
672 675 4.016444 TCCTCACAGACAAAGTTTGCTTT 58.984 39.130 15.59 4.50 45.04 3.51
691 694 6.939163 GTCTACATGCATGGAATTAATCTCCT 59.061 38.462 29.41 7.20 33.77 3.69
725 1397 1.448119 GCTAATTCCTTCGGCTGGCC 61.448 60.000 0.00 0.00 0.00 5.36
890 1572 3.436470 GGGGGCCAAAGCTGATAGATTTA 60.436 47.826 4.39 0.00 31.26 1.40
936 1618 1.552578 TATAGACGTGTGTGCAGGGT 58.447 50.000 0.00 0.00 35.03 4.34
1200 1882 1.207329 GAGTACTTGCTCGGGTGGATT 59.793 52.381 0.00 0.00 0.00 3.01
1280 1962 2.852180 TACCCGGCATCATCGTCGG 61.852 63.158 0.00 0.00 41.90 4.79
1350 2032 0.618458 GCACCATGGGAGACAGGTTA 59.382 55.000 18.09 0.00 31.10 2.85
1370 2052 0.870393 CAGCAGTTCGACAAGCACAT 59.130 50.000 5.15 0.00 0.00 3.21
1440 2122 3.607741 CTCAAACAGAGTCATGGCTGAT 58.392 45.455 3.48 0.00 39.62 2.90
1934 4354 0.386476 CCTTGCACCGCCGTAGTATA 59.614 55.000 0.00 0.00 0.00 1.47
1995 4415 2.431057 GTGACGTCCCAGAATCTACCAT 59.569 50.000 14.12 0.00 0.00 3.55
2432 9032 1.609501 TAGAGCTCGGCACAGGGTT 60.610 57.895 8.37 0.00 0.00 4.11
2459 9059 1.905894 TGCCCCCTTTCAAATAAAGGC 59.094 47.619 10.42 0.00 44.17 4.35
2611 9238 1.409064 TGATGTCCCGATCTGCAGTAC 59.591 52.381 14.67 8.14 0.00 2.73
2616 9243 1.148157 CGTGTGATGTCCCGATCTGC 61.148 60.000 0.00 0.00 0.00 4.26
2635 9262 2.033194 AACGTCTAAAGCAGGCCGC 61.033 57.895 11.02 11.02 42.91 6.53
2744 9371 1.966901 TATCGCCAATCGTGTGGGCT 61.967 55.000 8.82 0.00 45.53 5.19
2747 9374 4.213270 ACATATTTATCGCCAATCGTGTGG 59.787 41.667 3.14 3.14 42.05 4.17
2797 9424 4.411327 GCAGCAGCAAACATAAAATCGTA 58.589 39.130 0.00 0.00 41.58 3.43
2798 9425 3.244976 GCAGCAGCAAACATAAAATCGT 58.755 40.909 0.00 0.00 41.58 3.73
2799 9426 2.277057 CGCAGCAGCAAACATAAAATCG 59.723 45.455 0.82 0.00 42.27 3.34
2800 9427 3.244976 ACGCAGCAGCAAACATAAAATC 58.755 40.909 0.82 0.00 42.27 2.17
2801 9428 3.302365 ACGCAGCAGCAAACATAAAAT 57.698 38.095 0.82 0.00 42.27 1.82
2802 9429 2.791383 ACGCAGCAGCAAACATAAAA 57.209 40.000 0.82 0.00 42.27 1.52
2859 9486 9.243105 ACAGTAAGGTAGCACATTTTTATGATT 57.757 29.630 0.00 0.00 0.00 2.57
2860 9487 8.807948 ACAGTAAGGTAGCACATTTTTATGAT 57.192 30.769 0.00 0.00 0.00 2.45
2878 9505 0.859232 AAGCGTGCGACAACAGTAAG 59.141 50.000 0.00 0.00 0.00 2.34
2984 9844 2.515057 TGCGGAAACCTGTGCGTT 60.515 55.556 0.00 0.00 34.45 4.84
3138 9999 3.909651 ATTGGGGGTTGCCGGTGT 61.910 61.111 1.90 0.00 0.00 4.16
3140 10001 2.854300 GATCATTGGGGGTTGCCGGT 62.854 60.000 1.90 0.00 0.00 5.28
3141 10002 2.043046 ATCATTGGGGGTTGCCGG 60.043 61.111 0.00 0.00 0.00 6.13
3143 10004 0.614415 TGTGATCATTGGGGGTTGCC 60.614 55.000 0.00 0.00 0.00 4.52
3145 10006 2.431782 GGATTGTGATCATTGGGGGTTG 59.568 50.000 0.00 0.00 33.77 3.77
3148 10009 2.457813 TGGATTGTGATCATTGGGGG 57.542 50.000 0.00 0.00 33.77 5.40


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.